Molecular hopper lines up for DNA sequencing

Engineering nanomachines is challenging due to the constantly fluctuating nature of matter at the nanometre scale. Nano-engineers have long dreamed of developing nanoscale motors that can transport nanoscopic cargo along user-specified routes, similar to the transport of passengers and cargo using motorized vehicles. Now a team of scientists at the University of Oxford has taken a significant leap towards realizing this dream by engineering a molecular “hopper” that can be moved back-and-forth by a user along a pre-defined track. This development enables unprecedented precision in the transport of nanoscale cargo and opens the door to next-generation applications such as high-precision DNA sequencing (Science 10.1126/science.aat3872). The molecular hopper consists of a small molecule body containing a functional group called a thiol (one sulphur atom with a hydrogen attached to it). The body is linked to a piece of molecular cargo; in this case, the cargo was a 40-nucleotide DNA strand, but other types of cargo could be used. The track consists of five thiol groups patterned in a row (called “footholds”) precisely spaced just 0.7 nm apart from each other. When a hopper encounters a track, the sulphur atoms in the two thiol groups will lose their hydrogen atoms and bind to each other, forming a disulphide bond. The stability of this disulphide bond prevents the hopper from spontaneously popping off the track. However, the hopper can transition between footholds. In the same way that a thiol group can swap its hydrogen atom for another sulphur atom, a sulphur in a disulphide bond can swap its partner sulphur atom for a different sulphur atom, enabling it to move along the track. To control the direction of a hopper’s motion along a track, the team constrained the track within a protein nanopore and inserted the nanopore into a membrane that separates two fluid compartments. The nanopore is the only hole that connects the two compartments, so a voltage difference between the two compartments (which the researchers generated using a conventional electrode setup) results in an electric field inside the nanopore. This electric field applies a force to the molecular hopper, shifting its position forward or backward depending upon the direction of the electric field. In other words, a hopper connected to foothold 1 will be pulled closer to foothold 2, significantly increasing its rate of transition from foothold 1 to foothold 2. Then, after the hopper transitions to foothold 2, the electric field will continue to act on it, pushing it closer to foothold 3. This process will continue until the hopper reaches the end of the track (foothold 5), at which point the researchers could reverse the electric field to make the hopper move backwards down the track. In this manner, the hopper can be moved back and forth across the nanoscale track for hundreds of steps. The hopper’s motion can be monitored by measuring the current flowing between the two fluid compartments. Because the nanopore is the only path through which current can flow, current measurements are highly sensitive to changes in the position of the hopper. When the researchers applied an electric field and continuously monitored the current, they observed five discrete current levels separated by sharp steps, corresponding to the walker transitioning between the five distinct footholds. This technology has a promising future. One upcoming application will likely be for DNA sequencing. As a proof-of-concept, the team used three slightly different DNA sequences as molecular cargo and found that they each provided unique current recordings. This was likely due to the sensitivity of current flow through the nanopore to the size and exact chemical structure of the hopper–cargo complex. High-throughput DNA sequencing would likely require the development of longer tracks. More generally, this work represents a significant advancement in the field of nanotechnology and will help to pave the way for engineered nanomachines of the future.